Characterizing the fecal bacteria and archaea community of heifers and lactating cows through 16S rRNA next-generation s
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ANIMAL GENETICS • ORIGINAL PAPER
Characterizing the fecal bacteria and archaea community of heifers and lactating cows through 16S rRNA next-generation sequencing Filippo Cendron 1
&
Giovanni Niero 1 & Gabriele Carlino 1 & Mauro Penasa 1 & Martino Cassandro 1
Received: 2 April 2020 / Revised: 29 June 2020 / Accepted: 11 August 2020 # The Author(s) 2020
Abstract The aim of this study was to describe the fecal bacteria and archaea composition of Holstein-Friesian and Simmental heifers and lactating cows, using 16S rRNA gene sequencing. Bacteria and archaea communities were characterized and compared between heifers and cows of the same breed. Two breeds from different farms were considered, just to speculate about the conservation of the microbiome differences between cows and heifers that undergo different management conditions. The two breeds were from two different herds. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the most abundant phyla in all experimental groups. Alpha- and beta-diversity metrics showed significant differences between heifers and cows within the same breed, supported by principal coordinate analysis. The analysis of Holstein-Friesian fecal microbiome composition revealed 3 different bacteria families, 2 genera, and 2 species that differed between heifers and cows; on the other hand, Simmental heifers and cows differed only for one bacteria family, one archaeal genus, and one bacteria species. Results of the present study suggest that fecal communities of heifers and cows are different, and that fecal microbiome is maintained across experimental groups. Keywords Dairy and dual-purpose breeds . Efficiency . Feces . Microbiome
Introduction The fecal microbiome consists of a complex community of microorganisms and represents a central issue in relation to cattle welfare and feed efficiency. In particular, the associations between fecal microbiome and animal health have been shown in the intestinal microbiota of calves (Oikonomou et al. 2013). The main factor that influences fecal microbiome composition is animal diet. Callaway et al. (2010) carried out an evaluation of bacterial diversity of 6 cattle (3 Jersey cows and 3 Angus steers) through a comparison of 3 different diets in terms of amount of dried distillers grain; Shanks et al. (2011) analyzed the structure of fecal community in 30 adult beef cattle equally divided in 3 diet groups; and Rice et al. (2012) evaluated the influence of different types and amount of
Communicated by: Maciej Szydlowski * Filippo Cendron [email protected] 1
Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell’Università, 16, 35020 Legnaro, PD, Italy
distillers grains on fecal microbial assemblages in 20 crossbreed cattle. The forage to concentrates ratio in the diet is the major factor affecting fecal microbiome composition in cattle (Kim et al. 2014). According to the meta-analysis of Kim and Wells (2016), the fecal cattle microbiome is composed of 10 phyla, 17 classes, 28
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